4RQU

Alcohol Dehydrogenase crystal structure in complex with NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.179 

wwPDB Validation 3D Report Full Report



Literature

Structural insight into the conformational change of alcohol dehydrogenase from arabidopsis Thalianal during coenzyme binding.

Chen, F.Wang, P.An, Y.Huang, J.Xu, Y.

(2014) Biochimie 108C: 33-39

  • DOI: 10.1016/j.biochi.2014.10.023
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Alcohol dehydrogenase (ADH, EC 1.1.1.1) plays important roles in the metabolism of alcohols and aldehydes. They are often subjected to conformational changes that are critical for the enzymatic activity and have received intensive investigation for h ...

    Alcohol dehydrogenase (ADH, EC 1.1.1.1) plays important roles in the metabolism of alcohols and aldehydes. They are often subjected to conformational changes that are critical for the enzymatic activity and have received intensive investigation for horse liver ADH. However, for the large plant ADH members, little is known regarding both the conformational change and its relationship to catalytic activity as plant ADH structures were rarely available. Here we describe three Arabidopsis ADH conformations obtained from two crystals, the apo crystal that was free of ligand, and the complex crystal that was with NAD. The NAD-complexed crystal yielded two different structural forms for the two subunits, one was occupied by the coenzyme, and the other was free and open. Structural comparisons demonstrate that the occupied subunit is in a closed conformation while the free subunit is fully open, and the apo structure in intermediate. Though all the forms have an overall fold similar to that of horse and human ADHs, the catalytic domain has an over 10° rotation. Additionally, unlike horse liver ADH, the loop (295-302aa) adopts different conformation. It does not rearrange upon the binding of the coenzyme norVal297 side chain experiences a flipping. Instead it always remains in the active site. His48 plays a switching role in the structure. Its imidazole ring has to swim away from the binding site to permit NAD binding. These together with the large differences in the substrate binding pocket, as well as in the proton relay system demonstrate that AtADH adopts a different catalysis mechanism from horse liver ADH.


    Organizational Affiliation

    The Nurturing Station for the State Key Laboratory of Subtropical Sylviculture, Zhejiang Agriculture and Forestry University, Lin'an, Zhejiang 311300, China. Electronic address: yxu@zafu.edu.cn.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alcohol DehydrogenaseA, B375Arabidopsis thalianaMutation(s): 0 
Gene Names: ADHADH1Arabidopsis thalianaAt1g77120F22K20.19
EC: 1.1.1.1
Find proteins for P06525 (Arabidopsis thaliana)
Explore P06525 
Go to UniProtKB:  P06525
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download CCD File 
B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NADKd:  1600000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.179 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.15α = 90
b = 101.15β = 90
c = 165.64γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHASESphasing
PHENIXrefinement
MOSFLMdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2014-11-05 
  • Released Date: 2014-12-17 
  • Deposition Author(s): Xu, Y.W.

Revision History 

  • Version 1.0: 2014-12-17
    Type: Initial release